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In this paper, the authors introduce local periodic perturbations of the cladding refractive index in the reduced diameter (waist) region of biconically tapered single-mode optical fibers by two methods. The first was focused ion beam milling to give short grooves perpendicular to the fiber axis, and the second was boron implantation, giving a phase grating in the cladding. Both structures exhibit a wavelength-dependent throughput and are highly sensitive to the environment in the waist region, which makes them potentially applicable in optical communication networks as well as in sensors. A simple corrugated slab-waveguide model is able to account for the measured spectral transmission of these structures.